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2009/7/31 Paul Emsley <[log in to unmask]>: > Alex Theodossis wrote: > >> >> Is it is possible to configure the Probe output in Coot not to display >> contact dots between atoms of the same residue? >> > > I don't see how to do that in probe, so I guess not. If you can persuade the > authors/maintainers of probe to create such an option, then Coot will > support it. > > Paul. > Probe provides a flexible way to define the source and the target atoms that are used to calculate overlaps. So if you wish to visualise the environment of a residue with probe dots, you could specify the residue itself as the source and the rest of the protein as the target. E.g. for chain A reisude 318: probe -once -u -stdbonds -mc "chainA 318" "not (chainA 318)" my-protein-with-H.pdb > my-probe-dots.out where my-protein-with-H.pdb is the output of reduce. Ultimately one could build up the whole interaction map residue-by-residue, appending the new dots onto the already existing ones -- I'd imagine that this wouldn't be too difficult. The resulting dots can be read in like this: (handle-read-draw-probe-dots-unformatted "path/to/the/probe-dots.out" imol 1) where imol is the reduced model's imol. But I do agree with Frank that this would be a rather esoteric way of using coot/reduce/probe... JED. ps. for those who love to misuse coot in esoteric ways: wait until coot switches to guile 1.9 (or above) -- that comes with a brainfuck compiler embedded.... http://wingolog.org/archives/2009/07/26/the-good-hack